BN1546 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 4.1656e-07 2.3628e-04
Layer 5 4.2772e-07 1.9698e-04
Layer 3 4.3890e-06 2.6213e-02
Layer 6 6.5584e-06 2.3428e-03
Layer 2 1.7062e-02 4.6372e-01
WM 5.5574e-02 1.7909e-01
Layer 1 4.8026e-01 4.3700e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
LGALS1 Expression Distribution
Gene Specificity Score (GSS)
LGALS1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
LGALS1 Layer 5 2.6396 0.7537
SLC24A2 Layer 4 2.5273 0.7500
PCLO Layer 4 2.4785 0.7358
DCLK1 Layer 5 2.4238 0.7322
PFKP Layer 5 2.5566 0.7318
CAMK2G Layer 5 2.3926 0.7275
TTC9B Layer 4 2.4570 0.7257
RAB3C Layer 5 2.3750 0.7240
SNCA Layer 6 2.0625 0.7231
CPLX1 Layer 5 2.3281 0.7223
PCSK1 Layer 5 2.4844 0.7155
SATB1 Layer 4 2.4668 0.7120
BNIP3 Layer 5 2.3438 0.7089
MYO5A Layer 4 2.3594 0.7080
NUDT4 Layer 5 2.3438 0.7056
NEUROD2 Layer 5 2.3184 0.7027
TOLLIP Layer 5 2.3398 0.7017
DHCR24 Layer 5 2.3994 0.7001
LDHA Layer 5 2.1289 0.6988
STX1A Layer 5 2.3467 0.6981
HK1 Layer 5 2.3398 0.6971
SYT4 Layer 5 2.3623 0.6958
NCALD Layer 5 2.3086 0.6942
SLC6A17 Layer 4 2.4609 0.6931
TUBB3 Layer 5 2.3438 0.6919
SH3GL2 Layer 5 2.1621 0.6918
ITGB1BP1 Layer 5 2.1943 0.6897
IQSEC1 Layer 5 2.3281 0.6895
TCEAL7 Layer 4 2.3809 0.6893
CHGB Layer 5 2.2520 0.6878
SLC9A6 Layer 4 2.5059 0.6863
PPM1A Layer 4 2.5664 0.6862
PRDX5 Layer 4 2.3027 0.6859
MSMO1 Layer 5 2.1719 0.6859
ATP6V1A Layer 5 2.2715 0.6838
STRAP Layer 4 2.2871 0.6837
CDIP1 Layer 5 2.1816 0.6832
CDK14 Layer 5 2.2744 0.6831
PRUNE2 Layer 5 2.5605 0.6831
STK39 Layer 5 2.1602 0.6829
SEZ6L2 Layer 5 2.1973 0.6828
PID1 Layer 5 2.4336 0.6823
BSN Layer 5 2.1680 0.6819
CLSTN2 Layer 5 3.3945 0.6815
NCOA7 Layer 5 2.2598 0.6812
UBE2QL1 Layer 5 2.3574 0.6805
TBR1 Layer 5 2.2715 0.6800
MAGED1 Layer 5 2.1094 0.6797
PRKCE Layer 5 2.1250 0.6786
MPPED1 Layer 5 2.4150 0.6783

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1546
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1546_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1546/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1546/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1546/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1546/report/PD/BN1546_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1546/report/PD/BN1546_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:57:00
  • Number of Processes: 10
  • Spending Time: 0h 3m